We are going to have a short notebook to introduce people to Xenium data as a precursor to the neighborhood analysis notebook.
This should contain:
- Some explanation about input Xenium files
- Reading in the BRCA Xenium Dataset from
STexampleData
- Reading in the annotations from Janesick et al
- Prepping the SPE object, including lumping annotations
- Plot of the cell type annotations
- Filtering out cells with
SpaceTrooper 👩🚀
- Normalization
For reference, the full outline can be found here.
We are going to have a short notebook to introduce people to Xenium data as a precursor to the neighborhood analysis notebook.
This should contain:
STexampleDataSpaceTrooper👩🚀For reference, the full outline can be found here.